No. You cannot set transparency to the scene. Do you?
You can only set transparency to the ColorLayer or Sprites.

How to resolve such problems in future? Check the class properties.
CCScene is derived from CCNode. So you can check properties of CCNode that can support by CCScene. Opacity is not the property of CCNode and CCScene.

I’m afraid that current transition effects actually support scenes only. If a simple transition effect for a layer like slide left/right/top/bottom etc is enough for you then you could just implement it by yourself with CCMoveTo action.